GeneGeneInteR

GeneGeneInteR performs gene-gene interaction analysis for case-control association studies to detect and test interactions among single nucleotide polymorphisms (SNPs) and genes.

Key Features:

• SNP-SNP Interaction Tests (SSI): Aggregates interaction tests at the single nucleotide polymorphism (SNP) level to identify interactions between individual genetic variants.
• Gene-Gene Multidimensional Methods (GGI): Assesses interactions at the gene level using multidimensional methods to capture complex relationships beyond single SNP pairs.
• Statistical Genetics Framework: Applies statistical genetics principles for interaction testing, including SNP-level data aggregation and multidimensional gene interaction analyses.
• Integration with Bioconductor: Implemented as a Bioconductor package in R to enable interoperability with other genomic analysis packages.
• Graphical Display Tools: Provides functions to visualize interaction results for interpretation of complex interaction patterns.

Scientific Applications:

• Case-Control Association Studies: Detects and tests gene-gene and SNP-SNP interactions to investigate genetic associations with case-control phenotypes.
• Multifactorial Disease Research: Identifies interacting genetic factors that contribute to the genetic architecture of complex and multifactorial diseases.

Methodology:

Methods are grounded in statistical genetics and include SNP-level aggregation and multidimensional gene interaction analyses, implemented within Bioconductor in R.